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1.  Nitrogen Distribution and Cycling through Water Flows in a Subtropical Bamboo Forest under High Level of Atmospheric Deposition 
PLoS ONE  2013;8(10):e75862.
Background
The hydrological cycle is an important way of transportation and reallocation of reactive nitrogen (N) in forest ecosystems. However, under a high level of atmospheric N deposition, the N distribution and cycling through water flows in forest ecosystems especially in bamboo ecosystems are not well understood.
Methodology/Principal Findings
In order to investigate N fluxes through water flows in a Pleioblastus amarus bamboo forest, event rainfall/snowfall (precipitation, PP), throughfall (TF), stemflow (SF), surface runoff (SR), forest floor leachate (FFL), soil water at the depth of 40 cm (SW1) and 100 cm (SW2) were collected and measured through the whole year of 2009. Nitrogen distribution in different pools in this ecosystem was also measured. Mean N pools in vegetation and soil (0–1 m) were 351.7 and 7752.8 kg ha−1. Open field nitrogen deposition at the study site was 113.8 kg N ha−1 yr−1, which was one of the highest in the world. N-NH4+, N-NO3− and dissolved organic N (DON) accounted for 54%, 22% and 24% of total wet N deposition. Net canopy accumulated of N occurred with N-NO3− and DON but not N-NH4+. The flux of total dissolved N (TDN) to the forest floor was greater than that in open field precipitation by 17.7 kg N ha−1 yr−1, due to capture of dry and cloudwater deposition net of canopy uptake. There were significant negative exponential relationships between monthly water flow depths and monthly mean TDN concentrations in PP, TF, SR, FFL and SW1.
Conclusions/Significance
The open field nitrogen deposition through precipitation is very high over the world, which is the main way of reactive N input in this bamboo ecosystem. The water exchange and N consume mainly occurred in the litter floor layer and topsoil layer, where most of fine roots of bamboo distributed.
doi:10.1371/journal.pone.0075862
PMCID: PMC3795693  PMID: 24146784
2.  New insights into the fungal community from the raw genomic sequence data of fig wasp Ceratosolen solmsi 
BMC Microbiology  2015;15(1):27.
Background
To date, biologists have discovered a large amount of valuable information from assembled genomes, but the abundant microbial data that is hidden in the raw genomic sequence data of plants and animals is usually ignored. In this study, the richness and composition of fungal community were determined in the raw genomic sequence data of Ceratosolen solmsi (RGSD-CS).
Results
To avoid the interference from sequences of C. solmsi, the unmapped raw data (about 17.1%) was obtained by excluding the assembled genome of C. solmsi from RGSD-CS. Comparing two fungal reference datasets, internal transcribed spacer (ITS) and large ribosomal subunit (LSU) of rRNA, the ITS dataset discovered a more diverse fungal community and was therefore selected as the reference dataset for evaluating the fungal community based on the unmapped raw data. The threshold of 95% sequence identity revealed many more matched fungal reads and fungal richness in the unmapped raw data than those by identities above 95%. Based on the threshold of 95% sequence identity, the fungal community of RGSD-CS was primarily composed of Saccharomycetes (88.4%) and two other classes (Agaricomycetes and Sordariomycetes, 8.3% in total). Compared with the fungal community of other reported fig wasps, Agaricomycetes and Eurotiomycetes were found to be unique to C. solmsi. In addition, the ratio of total fungal reads to RGSD-CS was estimated to be at least 4.8 × 10−3, which indicated that a large amount of fungal data was contained in RGSD-CS. However, rarefaction measure indicated that a deeper sequencing coverage with RGSD-CS was required to discover the entire fungal community of C. solmsi.
Conclusion
This study investigated the richness and composition of fungal community in RGSD-CS and provided new insights into the efficient study of microbial diversity using raw genomic sequence data.
Electronic supplementary material
The online version of this article (doi:10.1186/s12866-015-0370-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12866-015-0370-3
PMCID: PMC4329198
Fungal community; Unmapped raw data; Fig wasp; Fungal reference datasets
3.  Inactivation of Sag/Rbx2/Roc2 E3 Ubiquitin Ligase Triggers Senescence and Inhibits Kras-Induced Immortalization 
Neoplasia (New York, N.Y.)  2015;17(1):114-123.
Our recent study showed that SAG/RBX2 E3 ubiquitin ligase regulates apoptosis and vasculogenesis by promoting degradation of NOXA and NF1, and co-operates with Kras to promote lung tumorigenesis by activating NFκB and mTOR pathways via targeted degradation of tumor suppressive substrates including IκB, DEPTOR, p21 and p27. Here we investigated the role of Sag/Rbx2 E3 ligase in cellular senescence and immortalization of mouse embryonic fibroblasts (MEFs) and report that Sag is required for proper cell proliferation and KrasG12D-induced immortalization. Sag inactivation by genetic deletion remarkably suppresses cell proliferation by inducing senescence, which is associated with accumulation of p16, but not p53. Mechanistically, Sag deletion caused accumulation of Jun-B, a substrate of Sag-Fbxw7 E3 ligase and a transcription factor that drives p16 transcription. Importantly, senescence triggered by Sag deletion can be largely rescued by simultaneous deletion of Cdkn2a, the p16 encoding gene, indicating its causal role. Furthermore, KrasG12D-induced immortalization can also be abrogated by Sag deletion via senescence induction, which is again rescued by simultaneous deletion of Cdkn2a. Finally, we found that Sag deletion inactivates KrasG12D activity and block the MAPK signaling pathway, together with accumulated p16, to induce senescence. Taken together, our results demonstrated that Sag is a KrasG12D-cooperating oncogene required for KrasG12D-induced immortalization and transformation, and targeting SAG-SCF E3 ligase may, therefore, have therapeutic value for senescence-based cancer treatment.
doi:10.1016/j.neo.2014.11.008
PMCID: PMC4309684  PMID: 25622904
4.  Identification of ribonucleotide reductase M2 as a potential target for pro-senescence therapy in epithelial ovarian cancer 
Cell Cycle  2013;13(2):199-207.
Epithelial ovarian cancer (EOC) is the leading cause of gynecological-related cancer deaths in the United States. There is, therefore, an urgent need to develop novel therapeutic strategies for this devastating disease. Cellular senescence is a state of stable cell growth arrest that acts as an important tumor suppression mechanism. Ribonucleotide reductase M2 (RRM2) plays a key role in regulating the senescence-associated cell growth arrest by controlling biogenesis of 2'-deoxyribonucleoside 5′-triphosphates (dNTPs). The role of RRM2 in EOC remains poorly understood. Here we show that RRM2 is expressed at higher levels in EOCs compared with either normal ovarian surface epithelium (P < 0.001) or fallopian tube epithelium (P < 0.001). RRM2 expression significantly correlates with the expression of Ki67, a marker of cell proliferation (P < 0.001). Moreover, RRM2 expression positively correlates with tumor grade and stage, and high RRM2 expression independently predicts a shorter overall survival in EOC patients (P < 0.001). To delineate the functional role of RRM2 in EOC, we knocked down RRM2 expression in a panel of EOC cell lines. Knockdown of RRM2 expression inhibits the growth of human EOC cells. Mechanistically, RRM2 knockdown triggers cellular senescence in these cells. Notably, this correlates with the induction of the DNA damage response, a known mediator of cellular senescence. These data suggest that targeting RRM2 in EOCs by suppressing its activity is a novel pro-senescence therapeutic strategy that has the potential to improve survival of EOC patients.
doi:10.4161/cc.26953
PMCID: PMC3906237  PMID: 24200970
epithelial ovarian cancer; cellular senescence; ribonucleotide reductase M2 (RRM2); DNA damage response; cell proliferation
5.  Autoantibodies in Chinese patients with chronic hepatitis B: Prevalence and clinical associations 
AIM: To investigate the prevalence of autoantibodies and their associations with clinical features in Chinese patients with chronic hepatitis B (CHB).
METHODS: A total of 325 Chinese patients with CHB were enrolled in this retrospective, hospital-based study. Patients with chronic hepatitis C (CHC), autoimmune hepatitis (AIH), or primary biliary cirrhosis (PBC) were included, with healthy donors acting as controls. A panel of autoantibodies that serologically define AIH and PBC was tested by indirect immunofluorescence assay and line immunoassay. The AIH-related autoantibody profile included homogeneous anti-nuclear antibodies (ANA-H), smooth-muscle antibodies, anti-liver kidney microsome type 1, anti-liver cytosolic antigen type 1, and anti-soluble liver antigen/liver pancreas; the PBC-related antibodies were characterized by ANA-nuclear dots/membranous rim-like, anti-mitochondrial antibodies-M2 (AMA-M2), anti-BPO (recombinant antigen targeted by AMA-M2), anti-Sp100, anti-promyelocytic leukemia protein (anti-PML), and anti-gp210. The dichotomization of clustering was used to unequivocally designate the AIH or PBC profiles for each case. Anti-Ro52 antibodies were also tested.
RESULTS: The prevalence of any autoantibody in CHB amounted to 58.2%, which was similar to the 66.2% prevalence in CHC, significantly higher than the 6.7% in the healthy controls (P < 0.001), and lower than the 100% found in AIH and PBC (P = 0.004 and P < 0.001, respectively). There were more anti-PML and anti-gp210 antibodies among the CHB patients than the CHC patients (11.1% vs 0%, P = 0.003; 12.6% vs 0%, P < 0.001, respectively). The prevalence and titer of AMA, anti-BPO, anti-PML, and anti-gp210 were higher in PBC than in those with CHB. Among the CHB patients, the prevalence of ANA, especially ANA-H, was significantly lower in patients with compensated and decompensated cirrhosis compared with patients without cirrhosis. Thirty-eight cases of hepatocellular carcinoma (HCC) in CHB showed a significant difference compared with non-HCC patients in the prevalence of anti-PML (0% vs 12.5%, P = 0.013). Dichotomization of the autoantibodies revealed that the PBC profile was more prevalent in patients with CHB than in those with CHC, and that it was strongly correlated with both compensated and decompensated cirrhosis. In contrast, the prevalence of the AIH profile was significantly higher in non-cirrhosis patients with CHB than in those with compensated cirrhosis (18.5% vs 8.2%, P = 0.039). Moreover, the AIH profile was also closely associated with hepatitis B e-antigen positivity.
CONCLUSION: ANA-H could be an indicator of early-stage CHB. Dichotomizing the autoantibody profiles revealed that the PBC profile is strongly associated with cirrhosis in CHB.
doi:10.3748/wjg.v21.i1.283
PMCID: PMC4284347  PMID: 25574103
Autoantibodies; Chronic hepatitis B; Autoimmune hepatitis; Primary biliary cirrhosis; Cirrhosis; Hepatocellular carcinoma
6.  Bottlenecks in erucic acid accumulation in genetically engineered ultrahigh erucic acid Crambe abyssinica 
Plant Biotechnology Journal  2013;12(2):193-203.
Erucic acid is a valuable industrial fatty acid with many applications. The main producers of this acid are today high erucic rapeseed (Brassica napus) and mustard (Brassica juncea), which have 45%–50% of erucic acid in their seed oils. Crambe abyssinica is an alternative promising producer of this acid as it has 55%–60% of erucic acid in its oil. Through genetic modification (GM) of three genes, we have previously increased the level of erucic acid to 71% (68 mol%) in Crambe seed oil. In this study, we further investigated different aspects of oil biosynthesis in the developing GM Crambe seeds in comparison with wild-type (Wt) Crambe, rapeseed and safflower (Carthamus tinctorius). We show that Crambe seeds have very low phosphatidylcholine-diacylglycerol interconversion, suggesting it to be the main reason why erucic acid is limited in the membrane lipids during oil biosynthesis. We further show that GM Crambe seeds have slower seed development than Wt, accompanied by slower oil accumulation during the first 20 days after flowering (DAF). Despite low accumulation of erucic acid during early stages of GM seed development, nearly 86 mol% of all fatty acids accumulated between 27 and 50 DAF was erucic acid, when 40% of the total oil is laid down. Likely bottlenecks in the accumulation of erucic acid during early stages of GM Crambe seed development are discussed.
doi:10.1111/pbi.12128
PMCID: PMC4286110  PMID: 24119222
erucic acid; seed oil; Crambe abyssinica; biosynthesis; acylation; enzymes
7.  Thymoquinone-Loaded Nanostructured Lipid Carrier Exhibited Cytotoxicity towards Breast Cancer Cell Lines (MDA-MB-231 and MCF-7) and Cervical Cancer Cell Lines (HeLa and SiHa) 
BioMed Research International  2015;2015:263131.
Thymoquinone (TQ) has been shown to exhibit antitumor properties. Thymoquinone-loaded nanostructured lipid carrier (TQ-NLC) was developed to improve the bioavailability and cytotoxicity of TQ. This study was conducted to determine the cytotoxic effects of TQ-NLC on breast cancer (MDA-MB-231 and MCF-7) and cervical cancer cell lines (HeLa and SiHa). TQ-NLC was prepared by applying the hot high pressure homogenization technique. The mean particle size of TQ-NLC was 35.66 ± 0.1235 nm with a narrow polydispersity index (PDI) lower than 0.25. The zeta potential of TQ-NLC was greater than −30 mV. Polysorbate 80 helps to increase the stability of TQ-NLC. Differential scanning calorimetry showed that TQ-NLC has a melting point of 56.73°C, which is lower than that of the bulk material. The encapsulation efficiency of TQ in TQ-NLC was 97.63 ± 0.1798% as determined by HPLC analysis. TQ-NLC exhibited antiproliferative activity towards all the cell lines in a dose-dependent manner which was most cytotoxic towards MDA-MB-231 cells. Cell shrinkage was noted following treatment of MDA-MB-231 cells with TQ-NLC with an increase of apoptotic cell population (P < 0.05). TQ-NLC also induced cell cycle arrest. TQ-NLC was most cytotoxic towards MDA-MB-231 cells. It induced apoptosis and cell cycle arrest in the cells.
doi:10.1155/2015/263131
PMCID: PMC4303008  PMID: 25632388
8.  Full Endoscopic Transsphenoidal Surgery for Pituitary Adenoma-emphasized on Surgical Skill of Otolaryngologist 
The purpose is to summarize the experience in full endoscopic transsphenoidal resection of pituitary adenoma in 28 patients by rhinologist, and introduce the surgical skill of otolaryngologist, especially skills and cautions when operating inside nose. We removed pituitary adenoma in 28 patients via entirely endoscopic transsphenoidal approach with the help of special-designed instruments; we performed the procedure bloodlessly within limited time. The skill emphasized bilateral nostrils and four hands technique which was as delicate as possible not to scratch nasal mucosa or injure nasal frame. The special instruments included curette with suction, monopolar electrotome and bipolar coagulation forceps with suction, powered surgical equipments (Diamond Bur, Irrigation Tubing for Blades and Burs for nasal endoscopic surgery). Among 28 patients, there were 16 total resections, 8 subtotal resections, 3 partial resections, and 1 only biopsy due to excessive bleeding and hard nature. Of 19 patients with preoperative visual impairment, 12 patients had postoperative improvement in visual acuity and visual field. All the procedures were finished within 60 to 90 min. Complications seldom occurred except transient diabetes insipidus, especially no nasal-related signs or complications but 1 had epistaxis. The full endoscopic transsphenoidal surgery is a promising approach for pituitary adenoma resection. Multidisciplinary collaboration will lead to optimal cure for the patients. New technique and special-designed instruments can facilitate greatly this procedure.
doi:10.1007/s12070-011-0317-4
PMCID: PMC3918297  PMID: 24533411
Nasal endoscopy; Pituitary adenoma; Complication; Surgical skill
9.  Abnormal Pulmonary Function and Respiratory Muscle Strength Findings in Chinese Patients with Parkinson’s Disease and Multiple System Atrophy–Comparison with Normal Elderly 
PLoS ONE  2014;9(12):e116123.
Background
There have been limited comparative data regarding the investigations on pulmonary and respiratory muscle function in the patients with different parkinsonism disorders such as Parkinson’s disease (PD) and multiple system atrophy (MSA) versus normal elderly. The present study is aiming to characterize the performance of pulmonary function and respiratory muscle strength in PD and MSA, and to investigate the association with severity of motor symptoms and disease duration.
Methods
Pulmonary function and respiratory muscle strength tests were performed in 30 patients with PD, 27 with MSA as well as in 20 age-, sex-, height-, weight-matched normal elderly controls. All the patients underwent United Parkinson’s disease rating scale (UPDRS) or united multiple system atrophy rating scale (UMSARS) separately as diagnosed.
Results
Vital capacity, forced expiratory volume in 1 second and forced vital capacity decreased, residual volume and ratio of residual volume to total lung capacity increased in both PD and MSA groups compared to controls (p<0.05). Diffusing capacity was decreased in the MSA group, compared with PD and normal elderly control groups (p<0.05). Respiratory muscle strength was lower in both PD and MSA groups than in controls (p<0.05). The values representing spirometry function and respiratory muscle strength were found to have a negative linear correlation with mean score of UPDRS-III in PD and mean score of UMSARS-I in MSA. Respiratory muscle strength showed a negative linear correlation with the mean score of UMSARS-II and disease duration in MSA patients.
Conclusions
These findings suggest that respiratory dysfunction is involved in PD and MSA. Respiratory muscle strength is remarkably reduced, and some of the parameters correlate with disease duration and illness severity. The compromised respiratory function in neurodegenerative disorders should be the focus of further researches.
doi:10.1371/journal.pone.0116123
PMCID: PMC4278864  PMID: 25546308
10.  T helper cell dysregulation with hepatitis B and rebalance with glucocorticoids 
World Journal of Gastroenterology : WJG  2014;20(48):18354-18359.
AIM: To investigate T helper 17/regulatory T cell alterations in early severe hepatitis B and the effect of glucocorticoids.
METHODS: The study included 20 patients in the early stage of severe hepatitis B (SHB) and 11 healthy controls. All patients had elevated T helper 17 (Th17) levels, decreased regulatory T (Treg) cell levels, and significant Th17/Treg ratios.
RESULTS: After glucocorticoid treatment, 16 patients showed improvement with significant decreases in Th17 levels, increases in Treg, and rebalanced Th17/Treg ratios. The four patients who showed no improvement had increases in both Th17 and Treg levels and an even higher Th17/Treg ratio than before.
CONCLUSION: Glucocorticoid treatment can rectify Th17/Treg dysregulation in patients with SHB.
doi:10.3748/wjg.v20.i48.18354
PMCID: PMC4277972  PMID: 25561802
Severe hepatitis B; T helper 17 cell; Regulatory T cell; Dysregulation; Glucocorticoid
11.  Surgical treatment for residual or recurrent strabismus 
Although the surgical treatment is a relatively effective and predictable method for correcting residual or recurrent strabismus, such as posterior fixation sutures, medial rectus marginal myotomy, unilateral or bilateral rectus re-recession and resection, unilateral lateral rectus recession and adjustable suture, no standard protocol is established for the surgical style. Different surgical approaches have been recommended for correcting residual or recurrent strabismus. The choice of the surgical procedure depends on the former operation pattern and the surgical dosages applied on the patients, residual or recurrent angle of deviation and the operator's preference and experience. This review attempts to outline recent publications and current opinion in the management of residual or recurrent esotropia and exotropia.
doi:10.3980/j.issn.2222-3959.2014.06.27
PMCID: PMC4270976  PMID: 25540765
esotropia; exotropia; recurrence surgery
12.  The relationship between glycemic variability and diabetic peripheral neuropathy in type 2 diabetes with well-controlled HbA1c 
Background
Diabetic peripheral neuropathy (DPN) is one of the most common microvascular complications of diabetes. Glycemic variability could be an independent risk factor for diabetes complications in addition to average glucose. Type 2 diabetes with well-controlled glycosylated hemoglobin A1c (HbA1c) may have different terms of glycemic variability and vascular complication consequences. The aim of the study is to investigate the relationship between glycemic variability and DPN in type 2 diabetes with well-controlled HbA1c (HbA1c < 7.0%).
Methods
45 type 2 diabetes with well-controlled HbA1c(HbA1c < 7.0%) and with DPN (DM/DPN group) were recruited in the study, and 45 type 2 diabetes with well-controlled HbA1c and without DPN (DM/–DPN group) were set as controls. The two groups were also matched for age and diabetic duration. Blood pressure, body mass index(BMI), insulin sensitivity index (Matsuda index, ISI), total cholesterol (TC), triglyceride (TG), high density lipoprotein cholesterol (HDLC), and low density lipoprotein cholesterol (LDLC) were tested in the two groups. And all patients were monitored using the continuous glucose monitoring (CGM) system for consecutive 72 hours. The multiple parameters of glycemic variability included the standard deviation of blood glucose (SDBG), mean of daily differences (MODD) and mean amplitude of glycemic excursions (MAGE).
Results
The DM/DPN group had a greater SDBG, MODD and MAGE, when compared to the DM/–DPN group (p < 0.05). BMI, TC, and LDLC of DM/DPN group were lower than those of DM/–DPN group (p < 0.05). The patients with hypoglycemia were comparable between the two groups (p > 0.05). Univariate analysis showed DPN was closely associated with BMI (OR 0.82, CI 0.72–0.94, p = 0.005), TC (OR 0.63, CI 0.42–0.93, p = 0.02), LDLC (OR 0.4, CI 0.20–0.80, p = 0.009), SDBG (OR 2.95, CI 1.55–5.61, p = 0.001), MODD (OR 4.38, CI 1.48–12.93, p = 0.008), MAGE (OR 2.18, CI 1.47–3.24, p < 0.001). Multivariate logistic regression analysis showed that MAGE (OR 2.05, CI 1.36–3.09, p = 0.001) and BMI (OR 0.85, CI 0.73–0.99, p = 0.033) were significantly correlating with DPN. Glycemic variability, evaluated by MAGE, was the most significantly independent risk factor for DPN.
Conclusions
There was a close relationship between glycemic variability evaluated by MAGE and DPN in type 2 diabetes with well-controlled HbA1c.
doi:10.1186/1758-5996-6-139
PMCID: PMC4272789  PMID: 25530811
Glycemic variability; Continuous glucose monitoring; Diabetic peripheral neuropathy; Type 2 diabetes
13.  Developmental Programming of Long Non-Coding RNAs during Postnatal Liver Maturation in Mice 
PLoS ONE  2014;9(12):e114917.
The liver is a vital organ with critical functions in metabolism, protein synthesis, and immune defense. Most of the liver functions are not mature at birth and many changes happen during postnatal liver development. However, it is unclear what changes occur in liver after birth, at what developmental stages they occur, and how the developmental processes are regulated. Long non-coding RNAs (lncRNAs) are involved in organ development and cell differentiation. Here, we analyzed the transcriptome of lncRNAs in mouse liver from perinatal (day −2) to adult (day 60) by RNA-Sequencing, with an attempt to understand the role of lncRNAs in liver maturation. We found around 15,000 genes expressed, including about 2,000 lncRNAs. Most lncRNAs were expressed at a lower level than coding RNAs. Both coding RNAs and lncRNAs displayed three major ontogenic patterns: enriched at neonatal, adolescent, or adult stages. Neighboring coding and non-coding RNAs showed the trend to exhibit highly correlated ontogenic expression patterns. Gene ontology (GO) analysis revealed that some lncRNAs enriched at neonatal ages have their neighbor protein coding genes also enriched at neonatal ages and associated with cell proliferation, immune activation related processes, tissue organization pathways, and hematopoiesis; other lncRNAs enriched at adolescent ages have their neighbor protein coding genes associated with different metabolic processes. These data reveal significant functional transition during postnatal liver development and imply the potential importance of lncRNAs in liver maturation.
doi:10.1371/journal.pone.0114917
PMCID: PMC4263710  PMID: 25503252
14.  Utilisation of adsorption and desorption for simultaneously improving protein crystallisation success rate and crystal quality 
Scientific Reports  2014;4:7308.
High-quality protein crystals of suitable size are an important prerequisite for applying X-ray crystallography to determine the 3-dimensional structure of proteins. However, it is often difficult to obtain protein crystals of appropriate size and quality because nucleation and growth processes can be unsuccessful. Here, we show that by adsorbing proteins onto porous polystyrene-divinylbenzene microspheres (SDB) floating on the surface of the crystallisation solution, a localised high supersaturation region at the surface of the microspheres and a low supersaturation region below the microspheres can coexist in a single solution. The crystals will easily nucleate in the region of high supersaturation, but when they grow to a certain size, they will sediment to the region of low supersaturation and continue to grow. In this way, the probability of crystallisation and crystal quality can be simultaneously increased in a single solution without changing other crystallisation parameters.
doi:10.1038/srep07308
PMCID: PMC4255177  PMID: 25471817
15.  Resources and Biological Activities of Natural Polyphenols 
Nutrients  2014;6(12):6020-6047.
The oxidative stress imposed by reactive oxygen species (ROS) plays an important role in many chronic and degenerative diseases. As an important category of phytochemicals, phenolic compounds universally exist in plants, and have been considered to have high antioxidant ability and free radical scavenging capacity, with the mechanism of inhibiting the enzymes responsible for ROS production and reducing highly oxidized ROS. Therefore, phenolic compounds have attracted increasing attention as potential agents for preventing and treating many oxidative stress-related diseases, such as cardiovascular diseases, cancer, ageing, diabetes mellitus and neurodegenerative diseases. This review summarizes current knowledge of natural polyphenols, including resource, bioactivities, bioavailability and potential toxicity.
doi:10.3390/nu6126020
PMCID: PMC4277013  PMID: 25533011
polyphenols; antioxidant; cardioprotection; anticancer; anti-inflammation; antimicrobial; bioavailability
16.  Clinicopathological correlates of Gli1 expression in a population-based cohort of patients with newly diagnosed bladder cancer 
Urologic oncology  2014;32(5):539-545.
Introduction
Dysregulation of the hedgehog signalling pathway has been linked to the development and progression of a variety of different human tumors including cancers of the skin, brain, colon, prostate, blood, and pancreas. We assessed the clinicopathological factors that are potentially related to expression of Gli1, the transcription factor that is thought to be the most reliable marker of hedgehog pathway activation in bladder cancer.
Methods
Bladder cancer cases were identified from the New Hampshire State Cancer Registry as histologically confirmed primary bladder cancer diagnosed between January 1, 2002, and July 31, 2004. Immunohistochemical analysis was performed on a tissue microarray to detect Gli1 and p53 expression in these bladder tumors. We computed odds ratios (ORs) and their 95% CIs for Gli1 positivity for pathological category using T category (from TNM), invasiveness, and grade with both the World Health Organization 1973 and World Health Organization International Society of Urological Pathology criteria. We calculated hazard ratios and their 95% CI for Gli1 positivity and recurrence for both Ta-category and invasive bladder tumors (T1+).
Results
A total of 194 men and 67 women, whose tumors were assessable for Gli1 staining, were included in the study. No appreciable differences in Gli1 staining were noted by sex, age, smoking status, or high-risk occupation. Ta-category tumors were more likely to stain for Gli1 as compared with T1-category tumors (adjusted OR = 0.38, CI: 0.17–0.87). Similarly, low-grade (grades 1–2) tumors were more likely to stain for Gli1 as compared with high-grade tumors (grade 3) (adjusted OR = 0.44, CI: 0.21–0.93). In a Cox proportional hazards regression analysis, non–muscle-invasive bladder tumors expressing Gli1 were less likely to recur (adjusted hazard ratio = 0.48; CI: 0.28–0.82; P < 0.05) than those in which Gli1 was absent.
Conclusion
Our findings indicate that Gli1 expression may be a marker of low-stage, low-grade bladder tumors and an indicator of a reduced risk of recurrence in this group.
doi:10.1016/j.urolonc.2014.03.006
PMCID: PMC4243987  PMID: 24856810
Gli1; Bladder neoplasm
17.  Enteric microbiota leads to new therapeutic strategies for ulcerative colitis 
World Journal of Gastroenterology : WJG  2014;20(42):15657-15663.
Ulcerative colitis (UC) is a leading form of inflammatory bowel disease that involves chronic relapsing or progressive inflammation. As a significant proportion of UC patients treated with conventional therapies do not achieve remission, there is a pressing need for the development of more effective therapies. The human gut contains a large, diverse, and dynamic population of microorganisms, collectively referred to as the enteric microbiota. There is a symbiotic relationship between the human host and the enteric microbiota, which provides nutrition, protection against pathogenic organisms, and promotes immune homeostasis. An imbalance of the normal enteric microbiota composition (termed dysbiosis) underlies the pathogenesis of UC. A reduction of enteric microbiota diversity has been observed in UC patients, mainly affecting the butyrate-producing bacteria, such as Faecalibacterium prausnitzii, which can repress pro-inflammatory cytokines. Many studies have shown that enteric microbiota plays an important role in anti-inflammatory and immunoregulatory activities, which can benefit UC patients. Therefore, manipulation of the dysbiosis is an attractive approach for UC therapy. Various therapies targeting a restoration of the enteric microbiota have shown efficacy in treating patients with active and chronic forms of UC. Such therapies include fecal microbiota transplantation, probiotics, prebiotics, antibiotics, helminth therapy, and dietary polyphenols, all of which can alter the abundance and composition of the enteric microbiota. Although there have been many large, randomized controlled clinical trials assessing these treatments, the effectiveness and safety of these bacteria-driven therapies need further evaluation. This review focuses on the important role that the enteric microbiota plays in maintaining intestinal homeostasis and discusses new therapeutic strategies targeting the enteric microbiota for UC.
doi:10.3748/wjg.v20.i42.15657
PMCID: PMC4229530  PMID: 25400449
Ulcerative colitis; Enteric microbiota; Dysbiosis; Probiotic; Fecal microbiota transplantation; Polyphenol
18.  Potential therapeutic mechanism of genistein in breast cancer involves inhibition of cell cycle regulation 
Molecular Medicine Reports  2014;11(3):1820-1826.
Genistein can prevent tumorigenesis and reduce the incidence of diseases that are dependent upon estrogen. Previous research, however, has shown that genistein can also increase the risk of breast cancer. Thus, the aim of the present study was to investigate the mechanism underlying the effect of genistein in breast cancer and to determine whether genistein produces a therapeutic effect or promotes the development of breast cancer. Gene microarray data obtained from three samples treated with alcohol (control group), three samples treated with 3 μmol/l genistein and three samples treated with 10 μmol/l genistein for 48 h, were downloaded from the Gene Expression Omnibus database. Analysis of the differentially expressed genes (DEGs) and functional enrichment in the two genistein groups was performed. The interaction networks of the DEGs were constructed and the overlapping network was extracted. Finally, the functions and pathways of the DEGs in the overlapping network were enriched. In total, 224 DEGs coexisted in the two genistein groups, and the most significant function of these was the cell cycle. The number and the fold change of expression values of the DEGs in the 10 μmol/l genistein group were significantly higher compared with that of the 3 μmol/l genistein group. The most significant function and pathway of the DEGs in the overlapping network was the cell cycle involving several genes, including GLIPR1, CDC20, BUB1, MCM2 and CCNB1. Thus, genistein stimulation resulted in gene expression changes in breast cancer cell lines and discrepancies increased with higher doses of genistein. The DEGs were most significantly associated with cell cycle regulation.
doi:10.3892/mmr.2014.2907
PMCID: PMC4270317  PMID: 25385471
genistein; breast cancer; differentially expressed genes; cell cycle
19.  Self-assembled monolayers of alkanethiolates on surface chemistry groups in osteosarcoma cells 
Molecular Medicine Reports  2014;11(2):975-981.
Cell biomedical behavior is influenced by a number of factors, and the extracellular matrix (ECM) of the cellular microenvironment affects certain cancer cells. In the current study, U-2OS cells were cultured on gold surfaces modified with different terminal chemical groups [methyl (-CH3), amino (-NH2), hydroxyl (-OH) and carboxyl (-COOH)]. The results revealed that different chemical surfaces convey different behaviors. The density of the different functional surfaces was confirmed by atomic force microscopy. Cell morphology, proliferation rate and cell cycle were investigated using scanning electron microscopy, cell counting and flow cytometry. In conclusion, the type of chemical group on a biomaterial is an important property for the growth of osteosarcoma cells; -NH2 and -COOH surfaces sustained visible cell adhesion and promoted cell growth.
doi:10.3892/mmr.2014.2876
PMCID: PMC4262499  PMID: 25373556
osteosarcoma; functional groups; self-assembled monolayers
20.  Interferon regulatory factor 9 is critical for neointima formation following vascular injury 
Nature Communications  2014;5:5160.
Interferon regulatory factor 9 (IRF9) has various biological functions and regulates cell survival; however, its role in vascular biology has not been explored. Here we demonstrate a critical role for IRF9 in mediating neointima formation following vascular injury. Notably, in mice, IRF9 ablation inhibits the proliferation and migration of vascular smooth muscle cells (VSMCs) and attenuates intimal thickening in response to injury, whereas IRF9 gain-of-function promotes VSMC proliferation and migration, which aggravates arterial narrowing. Mechanistically, we show that the transcription of the neointima formation modulator SIRT1 is directly inhibited by IRF9. Importantly, genetic manipulation of SIRT1 in smooth muscle cells or pharmacological modulation of SIRT1 activity largely reverses the neointima-forming effect of IRF9. Together, our findings suggest that IRF9 is a vascular injury-response molecule that promotes VSMC proliferation and implicate a hitherto unrecognized ‘IRF9–SIRT1 axis’ in vasculoproliferative pathology modulation.
Blood vessels respond to injury by thickening the supportive smooth muscle layer in a process known as neointima formation. Here the authors describe a novel regulatory pathway of neointima formation that involves a transcription factor, Interferon Regulating Factor 9, and its downstream target, the deacetylase SIRT1.
doi:10.1038/ncomms6160
PMCID: PMC4218966  PMID: 25319116
21.  Successful Treatment of Giant Basal Cell Carcinoma with Topical Imiquimod 5% Cream with Long Term Follow-up 
Indian Journal of Dermatology  2014;59(6):575-578.
The use of the topical Imiquimod 5% cream offers a noninvasive, nonsurgical, and an effective option for the treatment of primary small (<2 cm) superficial basal cell carcinoma (sBCC). However, reports about successful treatment of giant (>5 cm) BCC with topical Imiquimod 5% cream are rare. We present our experience in the treatment of two giant tumors (6 × 8 cm2, 5.2 × 4.2 cm2) of BCC on the face with Imiquimod 5% cream, 2 to 3 days/week for 12 weeks. Both the tumors were cured with clinical and pathological evidence, one with 6-year follow-up and the other with 3.5-year follow-up.
doi:10.4103/0019-5154.143520
PMCID: PMC4248494  PMID: 25484387
Giant basal cell carcinoma; Imiquimod; treatment
22.  Predictive Value of Decoy Receptor 3 in Postoperative Nosocomial Bacterial Meningitis 
Nosocomial bacterial meningitis requires timely treatment, but what is difficult is the prompt and accurate diagnosis of this disease. The aim of this study was to assess the potential role of decoy receptor 3 (DcR3) levels in the differentiation of bacterial meningitis from non-bacterial meningitis. A total of 123 patients were recruited in this study, among them 80 patients being with bacterial meningitis and 43 patients with non-bacterial meningitis. Bacterial meningitis was confirmed by bacterial culture of cerebrospinal fluid (CSF) culture and enzyme-linked immunosorbent assay (ELISA) was used to detect the level of DcR3 in CSF. CSF levels of DcR3 were statistically significant between patients with bacterial meningitis and those with non-bacterial meningitis (p < 0.001). A total of 48.75% of patients with bacterial meningitis received antibiotic >24 h before CSF sampling, which was much higher than that of non-bacterial meningitis. CSF leucocyte count yielded the highest diagnostic value, with an area under the receiver operating characteristic curve (ROC) of 0.928, followed by DcR3. At a critical value of 0.201 ng/mL for DcR3, the sensitivity and specificity were 78.75% and 81.40% respectively. DcR3 in CSF may be a valuable predictor for differentiating patients with bacterial meningitis from those with non-bacterial meningitis. Further studies are needed for the validation of this study.
doi:10.3390/ijms151119962
PMCID: PMC4264149  PMID: 25372942
decoy receptor 3; DcR3; bacterial meningitis; diagnosis
23.  Comparison of the Efficacy of Rosuvastatin versus Atorvastatin in Preventing Contrast Induced Nephropathy in Patient with Chronic Kidney Disease Undergoing Percutaneous Coronary Intervention 
PLoS ONE  2014;9(10):e111124.
Objectives
We prospectively compared the preventive effects of rosuvastatin and atorvastatin on contrast-induced nephropathy (CIN) in patients with chronic kidney disease (CKD) undergoing percutaneous coronary intervention (PCI).
Methods
We enrolled 1078 consecutive patients with CKD undergoing elective PCI. Patients in Group 1 (n = 273) received rosuvastatin (10 mg), and those in group 2 (n = 805) received atorvastatin (20 mg). The primary end-point was the development of CIN, defined as an absolute increase in serum creatinine ≥0.5 mg/dL, or an increase ≥25% from baseline within 48–72 h after contrast medium exposure.
Results
CIN was observed in 58 (5.4%) patients. The incidence of CIN was similar in patients pretreated with either rosuvastatin or atorvastatin (5.9% vs. 5.2%, p = 0.684). The same results were also observed when using other definitions of CIN. Clinical and procedural characteristics did not show significant differences between the two groups (p>0.05). Additionally, there were no significant inter-group differences with respect to in-hospital mortality rates (0.4% vs. 1.5%, p = 0.141), or other in-hospital complications. Multivariate logistic regression analysis revealed that rosuvastatin and atorvastatin demonstrated similar efficacies for preventing CIN, after adjusting for potential confounding risk factors (odds ratio = 1.17, 95% confidence interval, 0.62–2.20, p = 0.623). A Kaplan–Meier survival analysis showed that patients taking either rosuvastatin or atorvastatin had similar incidences of all-cause mortality (9.4% vs. 7.1%, respectively; p = 0.290) and major adverse cardiovascular events (29.32% vs. 23.14%, respectively; p = 0.135) during follow-up.
Conclusions
Rosuvastatin and atorvastatin have similar efficacies for preventing CIN in patients with CKD undergoing PCI.
doi:10.1371/journal.pone.0111124
PMCID: PMC4214705  PMID: 25357250
24.  Intestinal microbiota pathogenesis and fecal microbiota transplantation for inflammatory bowel disease 
World Journal of Gastroenterology : WJG  2014;20(40):14805-14820.
The intestinal microbiota plays an important role in inflammatory bowel disease (IBD). The pathogenesis of IBD involves inappropriate ongoing activation of the mucosal immune system driven by abnormal intestinal microbiota in genetically predisposed individuals. However, there are still no definitive microbial pathogens linked to the onset of IBD. The composition and function of the intestinal microbiota and their metabolites are indeed disturbed in IBD patients. The special alterations of gut microbiota associated with IBD remain to be evaluated. The microbial interactions and host-microbe immune interactions are still not clarified. Limitations of present probiotic products in IBD are mainly due to modest clinical efficacy, few available strains and no standardized administration. Fecal microbiota transplantation (FMT) may restore intestinal microbial homeostasis, and preliminary data have shown the clinical efficacy of FMT on refractory IBD or IBD combined with Clostridium difficile infection. Additionally, synthetic microbiota transplantation with the defined composition of fecal microbiota is also a promising therapeutic approach for IBD. However, FMT-related barriers, including the mechanism of restoring gut microbiota, standardized donor screening, fecal material preparation and administration, and long-term safety should be resolved. The role of intestinal microbiota and FMT in IBD should be further investigated by metagenomic and metatranscriptomic analyses combined with germ-free/human flora-associated animals and chemostat gut models.
doi:10.3748/wjg.v20.i40.14805
PMCID: PMC4209544  PMID: 25356041
Inflammatory bowel disease; Intestinal microbiota; Probiotics; Fecal microbiota transplantation; Synthetic microbiota transplantation
25.  Functional expression, characterization and application of the human S100A4 protein 
Molecular Medicine Reports  2014;11(1):175-181.
Preparations utilizing monoclonal antibodies against S100A4 provide useful tools for functional studies to investigate the clinical applications of the human S100A4 protein. In the present study, human S100A4 protein was expressed in Escherichia coli (E. coli) BL21 (DE3), successfully purified by diethylaminoethyl cellulose anion-exchange chromatography and identified by western blot analysis. Soluble S100A4 bioactivity was confirmed by Transwell migration and invasion assays in the human HeLa cell line. Monoclonal antibodies (mAbs) were generated utilizing the standard hybridoma method and were validated by enzyme-linked immunosorbent assay and western blot analysis. The antibody was then used to examine human gastric carcinoma specimens by immunohistochemistry. Recombinant S100A4 was functionally expressed in E. coli and promoted the migration and invasion of HeLa cells. Four hybridoma cell lines, which secreted mAbs specifically against human S100A4 protein, were obtained. One of the four mAbs, namely 2A12D10B2, recognized human S100A4 as indicated by immunohistochemical staining of human gastric carcinoma specimens and recombinant S100A4 was functionally expressed in E. coli. The mAbs of recombinant S100A4 were suitable for detecting S100A4 expression in human tissues and for investigating the subsequent clinical applications of the protein.
doi:10.3892/mmr.2014.2745
PMCID: PMC4237081  PMID: 25339497
human S100A4 protein; monoclonal antibody; preparation; application

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